diff --git a/java/base.go b/java/base.go
index c828503..25cc68f 100644
--- a/java/base.go
+++ b/java/base.go
@@ -1217,12 +1217,6 @@
 				return
 			}
 
-			// Initialize the hiddenapi structure.
-			j.initHiddenAPI(ctx, dexOutputFile, j.implementationJarFile, j.dexProperties.Uncompress_dex)
-
-			// Encode hidden API flags in dex file.
-			dexOutputFile = j.hiddenAPIEncodeDex(ctx, dexOutputFile)
-
 			// merge dex jar with resources if necessary
 			if j.resourceJar != nil {
 				jars := android.Paths{dexOutputFile, j.resourceJar}
@@ -1238,6 +1232,12 @@
 				}
 			}
 
+			// Initialize the hiddenapi structure.
+			j.initHiddenAPI(ctx, dexOutputFile, j.implementationJarFile, j.dexProperties.Uncompress_dex)
+
+			// Encode hidden API flags in dex file, if needed.
+			dexOutputFile = j.hiddenAPIEncodeDex(ctx, dexOutputFile)
+
 			j.dexJarFile = dexOutputFile
 
 			// Dexpreopting